process_10xh5/filter_10xh5

Description

Filter a 10x h5 dataset.

Type

r_script

License

MIT

Links

Repository

Contributors

Launch

Run this component

Run the following command to execute this component with Nextflow:

cat > params.yaml <<'EOM'  
output: "$id.$key.output.h5"  
min_library_size: [ 0 ]  
min_cells_per_gene: [ 0 ]  
id: "run"  
publish_dir: "output/"  
EOM

nextflow run https://packages.viash-hub.com/vsh/openpipeline.git \  
  -revision v4.0.2 \  
  -main-script target/nextflow/process_10xh5/filter_10xh5/main.nf \  
  -params-file params.yaml

Arguments

Name	Type & Properties	Description
--input	file required	An h5 file from the 10x genomics website.
--output	file required output	Output h5 file.
--min_library_size	integer	Minimum library size.
--min_cells_per_gene	integer	Minimum number of cells per gene.
--keep_feature_types	string multiple	Specify which feature types will never be filtered out
--verbose	boolean_true	Increase verbosity

Name

Type & Properties

--input

file

required

--output

file

required

output

--min_library_size

integer

--min_cells_per_gene

integer

--keep_feature_types

string

multiple

--verbose

boolean_true